PAFway

PAFway quantifies pairwise associations between functional annotations within biological networks and pathways to elucidate functional relationships and regulatory interactions.

Key Features:

• Pairwise Association Estimation: Estimates pairwise associations between functional annotations across biological networks and pathways.
• Biological Insight Generation: Identifies whether genes with specific functions tend to influence or interact with genes bearing different functions, supporting inference of regulatory mechanisms.
• Visualization Capabilities: Produces heatmaps and network diagrams of biological functions to represent complex associations.
• Application to Model Organisms: Has been applied to an Arabidopsis thaliana gene network.

Scientific Applications:

• Dissection of Gene Regulatory Networks: Supports identification and interpretation of functional associations within complex gene regulatory networks.
• Systems Biology: Enables systems biology analyses by mapping functional relationships across pathways.
• Gene Regulation Studies: Aids studies of gene regulation by revealing associative influences among functionally annotated genes.
• Network Biology and Functional Genomics: Supports network biology and functional genomics by enabling analysis and visualization of functional associations across pathways.

Methodology:

Calculates pairwise associations between functional annotations derived from biological networks and pathways and applies statistical techniques to assess the strength and significance of these associations.